豫农黑猪生长相关性状的拷贝数变异全基因组关联分析研究

doi:10.11843/j.issn.0366-6964.2025.03.013

Abstract

Abstract:

This study aimed to detect genome-wide copy number variations (CNVs) in Yunong-black pigs and identify candidate genes associated to growth-related traits in this breed. Growth-related traits were collected from 807 Yunong-black pigs (738 sows and 69 boars) across four generations (2rd-5th generation), with body weight range of 95 to 105 kg. The measured traits included body length (BL), body height (BH), chest circumference (CC), cannon bone circumference (CBC), legs buttocks circumference (LBC), backfat thickness (BF), and loin muscle depth (LMD). Ear tissue samples from the experimental population were genotyped using the "Zhongxin-1"50K SNP chip, and CNV detection was performed using PennCNV software. The CNV regions (CNVRs) were identified by merging overlapping CNVs and genome-wide association analysis (GWAS) was conducted using Plink software to examine associations between CNVs and growth-related traits. A total of 1 432 CNVs were identified on 18 autosomes and merged into 232 CNVRs. The CNVs ranged in size from 2.7 kb to 2.2 Mb, while CNVRs spanned from 4.5 kb to 2.2 Mb, covering 56.4 Mb or 2.50% of the autosomal genome. GWAS identified one CNV was associated with CC at the genome-wide significance level, and seven CNVs showed suggestive associated with CC, CBC and BF. The CNV most strongly associated with CC also showed a strong association with CBC. Additionally, the CLDN23 gene on SSC17 was significantly associated with BF, suggesting its potential role in regulating muscle development or fat deposition. This study provides new insights into the functional implications of CNVs in the Yunong-black pig, and offering valuable theoretical support for implement molecular marker-assisted selection in Yunong-black pigs breeding programs.

Key words: Yunong-black pigs, growth traits, copy number variation, genome-wide association study(GWAS)

CLC Number:

S828.2

WU Jiahao, WU Ziyi, DOU Tengfei, BAI Liyao, ZHANG Yongqian, DONG Lianhe, LI Pengfei, LI Xinjian, HAN Xuelei, LI Xiuling. Genome-wide Association Study of Copy Number Variation in Growth-Related Traits of Yunong-Black Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1110-1119.

Figures/Tables 6

Fig. 1

Table 1

Fig. 2

Fig. 3

Table 2

Fig. 4

References 47

1	许迪, 颜港, 张帅, 等. 大白猪生长性状影响因素分析及遗传参数估计[J]. 中国畜牧兽医, 2024, 51 (1): 193- 202.
	XU D , YAN G , ZHANG S , et al. Influencing factors analysis and genetic parameters estimation of growth traits in yorkshire pigs[J]. China Animal Husbandry & Veterinary Medicine, 2024, 51 (1): 193- 202.
2	康佳威, 黄宣凯, 王志鹏, 等. 大白猪生长、繁殖和体尺性状遗传参数估计[J]. 畜牧兽医学报, 2024, 55 (5): 1936- 1944.
	KANG J W , HUANG X K , WANG Z P , et al. Estimation of genetic parameters for growth, reproduction, and body measurements traits in large white pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55 (5): 1936- 1944.
3	王克君. 基于多重关联分析鉴定猪生长性状相关基因及其功能验证[D]. 北京: 中国农业大学, 2017.
	WANG K J. Identification of growth-related genes based on multi-association analysis and their potential gene function verification in pig[D]. Beijing: China Agricultural University, 2017. (in Chinese)
4	阮栋林, 陈悦, 庄站伟, 等. 基于SNP芯片的杜洛克种猪生长和体尺性状遗传参数估计及相关分析[J]. 家畜生态学报, 2023, 44 (2): 19- 24. doi: 10.3969/j.issn.1673-1182.2023.02.004
	RUAN D L , CHEN Y , ZHUANG Z W , et al. Genetic parameter estimation and correlation analysis of growth traits and body traits in duroc pigs based on SNP chip[J]. Acta Ecologae Animalis Domastici, 2023, 44 (2): 19- 24. doi: 10.3969/j.issn.1673-1182.2023.02.004
5	ZHOU J H , LIU L Y , REYNOLDS E , et al. Discovering copy number variation in dual-purpose XinJiang brown cattle[J]. Front Genet, 2022, 12, 747431. doi: 10.3389/fgene.2021.747431
6	HUANG Y Z , LI Y J , WANG X H , et al. An atlas of CNV maps in cattle, goat and sheep[J]. Sci China Life Sci, 2021, 64 (10): 1747- 1764. doi: 10.1007/s11427-020-1850-x
7	ZHANG W , ZHOU M , LIU L Q , et al. Population structure and selection signatures underlying domestication inferred from genome-wide copy number variations in Chinese indigenous pigs[J]. Genes (Basel), 2022, 13 (11): 2026. doi: 10.3390/genes13112026
8	CENDRON F , CASSANDRO M , PENASA M . Genome-wide investigation to assess copy number variants in the Italian local chicken population[J]. J Anim Sci Biotechnol, 2024, 15 (1): 2. doi: 10.1186/s40104-023-00965-7
9	DE OLIVEIRA H R , CHUD T C S , OLIVEIRA G A Jr , et al. Genome-wide association analyses reveal copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle[J]. J Dairy Sci, 2024, 107 (9): 7052- 7063.
10	饶友生, 张细权. 拷贝数目变异: 基因组遗传变异的新诠释[J]. 生物多样性, 2008, 16 (4): 399- 406. doi: 10.3321/j.issn:1005-0094.2008.04.011
	RAO Y S , ZHANG X Q . Copy-number variant: new annotation for genetic variation across genomes[J]. Biodiversity Science, 2008, 16 (4): 399- 406. doi: 10.3321/j.issn:1005-0094.2008.04.011
11	BICKHART D M , LIU G E . The challenges and importance of structural variation detection in livestock[J]. Front Genet, 2014, 5, 37.
12	GARRICK D J , TAYLOR J F , FERNANDO R L . Deregressing estimated breeding values and weighting information for genomic regression analyses[J]. Genet Sel Evol, 2009, 41 (1): 55. doi: 10.1186/1297-9686-41-55
13	WONG K K , DELEEUW R J , DOSANJH N S , et al. A comprehensive analysis of common copy-number variations in the human genome[J]. Am J Hum Genet, 2007, 80 (1): 91- 104. doi: 10.1086/510560
14	FADISTA J , NYGAARD M , HOLM L E , et al. A snapshot of CNVs in the pig genome[J]. PLoS One, 2008, 3 (12): e3916. doi: 10.1371/journal.pone.0003916
15	RAMAYO-CALDAS Y , CASTELLÓ A , PENA R N , et al. Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip[J]. BMC Genomics, 2010, 11, 593. doi: 10.1186/1471-2164-11-593
16	CHEN C Y , QIAO R M , WEI R X , et al. A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits[J]. BMC Genomics, 2012, 13, 733. doi: 10.1186/1471-2164-13-733
17	WANG L G , XU L Y , LIU X , et al. Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in swine[J]. Sci Rep, 2015, 5, 12535. doi: 10.1038/srep12535
18	QIAN R , XIE F , ZHANG W , et al. Genome-wide detection of CNV regions between Anqing six-end-white and Duroc pigs[J]. Mol Cytogenet, 2023, 16 (1): 12. doi: 10.1186/s13039-023-00646-0
19	REVILLA M , PUIG-OLIVERAS A , CASTELLÓ A , et al. A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits[J]. PLoS One, 2017, 12 (5): e0177014. doi: 10.1371/journal.pone.0177014
20	王明宇, 张晨, 叶建伟, 等. 雏鹰黑猪血液生理指标与肉质性状及屠宰性能间的相关性分析[J]. 家畜生态学报, 2018, 39 (12): 38- 43. doi: 10.3969/j.issn.1673-1182.2018.12.007
	WANG M Y , ZHANG C , YE J W , et al. Correlation analysis between blood physiological indexes and meat ouality traits and slaughter performance of chuying black pigs[J]. Acta Ecologiae Animalis Domastici, 2018, 39 (12): 38- 43. doi: 10.3969/j.issn.1673-1182.2018.12.007
21	薛亚辉, 王明宇, 张晨, 等. 雏鹰黑猪与确山黑猪血液生理指标及其与生产性能的相关性分析[J]. 河南农业大学学报, 2019, 53 (6): 884- 890.
	XUE Y H , WANG M Y , ZHANG C , et al. Correlation between blood physiological indexes and production performance in Chuying Black Pig and Queshan Black Pig[J]. Journal of Henan Agricultural University, 2019, 53 (6): 884- 890.
22	OGAWA S , YAZAKI N , OHNISHI C , et al. Maternal effect on body measurement and meat production traits in purebred Duroc pigs[J]. J Anim Breed Genet, 2021, 138 (2): 237- 245.
23	XUE Y , LI C , DUAN D , et al. Genome-wide association studies for growth-related traits in a crossbreed pig population[J]. Anim Genet, 2021, 52 (2): 217- 222. doi: 10.1111/age.13032
24	WU Z Y , DOU T F , BAI L Y , et al. Genomic prediction and genome-wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high-density SNP genotypes in Yunong-black pigs[J]. J Anim Breed Genet, 2024, 141 (2): 124- 137. doi: 10.1111/jbg.12830
25	WANG K , LI M Y , HADLEY D , et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data[J]. Genome Res, 2007, 17 (11): 1665- 1674. doi: 10.1101/gr.6861907
26	ZHOU J H , LIU L Y , LOPDELL T J , et al. HandyCNV: standardized summary, annotation, comparison, and visualization of copy number variant, copy number variation region, and runs of homozygosity[J]. Front Genet, 2021, 12, 731355. doi: 10.3389/fgene.2021.731355
27	YANG Q , CUI J , CHAZARO I , et al. Power and type Ⅰ error rate of false discovery rate approaches in genome-wide association studies[J]. BMC Genet, 2005, 6 (S1): S134. doi: 10.1186/1471-2156-6-S1-S134
28	HU Z L , PARK C A , REECY J M . Bringing the animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services[J]. Nucleic Acids Res, 2022, 50 (D1): D956- D961.
29	TENG J Y , GAO Y H , YIN H W , et al. A compendium of genetic regulatory effects across pig tissues[J]. Nat Genet, 2024, 56 (1): 112- 123. doi: 10.1038/s41588-023-01585-7
30	ABDELLAOUI A , YENGO L , VERWEIJ K J H , et al. 15 years of GWAS discovery: realizing the promise[J]. Am J Hum Genet, 2023, 110 (2): 179- 194.
31	MANOLIO T A , COLLINS F S , COX N J , et al. Finding the missing heritability of complex diseases[J]. Nature, 2009, 461 (7265): 747- 753.
32	MAHER B . Personal genomes: the case of the missing heritability[J]. Nature, 2008, 456 (7218): 18- 21.
33	SALEHIAN-DEHKORDI H , XU Y X , XU S S , et al. Genome-wide detection of copy number variations and their association with distinct phenotypes in the world 's sheep[J]. Front Genet, 2021, 12, 670582.
34	TAGHIZADEH S , GHOLIZADEH M , RAHIMI-MIANJI G , et al. Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds[J]. Sci Rep, 2022, 12 (1): 8834.
35	XU L Y , YANG L , WANG L , et al. Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle[J]. BMC Genomics, 2019, 20 (1): 31.
36	SHI H B , LI T T , SU M C , et al. Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection[J]. BMC Genomics, 2023, 24 (1): 555.
37	DING R R , ZHUANG Z W , QIU Y B , et al. Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis[J]. J Anim Sci, 2022, 100 (2): skac012.
38	LEE G J , ARCHIBALD A L , GARTH G B , et al. Detection of quantitative trait loci for locomotion and osteochondrosis-related traits in Large White×Meishan pigs[J]. Anim Sci, 2003, 76 (2): 155- 165.
39	CASSADY J P , JOHNSON R K , POMP D , et al. Identification of quantitative trait loci affecting reproduction in pigs[J]. J Anim Sci, 2001, 79 (3): 623- 633.
40	HOWARD J T , JIAO S H , TIEZZI F , et al. Genome-wide association study on legendre random regression coefficients for the growth and feed intake trajectory on Duroc Boars[J]. BMC Genet, 2015, 16, 59.
41	TRIBOUT T , IANNUCCELLI N , DRUET T , et al. Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations[J]. Genet Sel Evol, 2008, 40 (1): 61- 78.
42	CHEREL P , PIRES J , GLÉNISSON J , et al. Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs[J]. BMC Genet, 2011, 12, 76.
43	LIU G S , KIM J J , JONAS E , et al. Combined line-cross and half-sib QTL analysis in Duroc-Pietrain population[J]. Mamm Genome, 2008, 19 (6): 429- 438.
44	WON S , JUNG J , PARK E , et al. Identification of genes related to intramuscular fat content of pigs using genome-wide association study[J]. Asian-Australas J Anim Sci, 2018, 31 (2): 157- 162.
45	KUO I H , CARPENTER-MENDINI A , YOSHIDA T , et al. Activation of epidermal toll-like receptor 2 enhances tight junction function: implications for atopic dermatitis and skin barrier repair[J]. J Invest Dermatol, 2013, 133 (4): 988- 998.
46	LIU X K , BING Z T , WU J R , et al. Integrative gene expression profiling analysis to investigate potential prognostic biomarkers for colorectal cancer[J]. Med Sci Monit, 2020, 26, e918906.
47	YANG H J , LIU H , LIN H C , et al. Association of a novel seven-gene expression signature with the disease prognosis in colon cancer patients[J]. Aging (Albany NY), 2019, 11 (19): 8710- 8727.

染色体 Chromosome	CNVR数目 CNVR count	CNVR长度/kb Length of CNVR	最小长度/kb Minimum size	最大长度/kb Maximum size	平均长度/kb Average size
1	18	4 246.27	9.30	1 465.44	235.90
2	18	4 847.94	31.11	704.46	269.33
3	18	5 953.04	43.95	1 141.00	330.72
4	9	3 649.12	28.24	2 222.16	405.46
5	9	2 699.64	41.88	652.15	299.96
6	15	5 653.12	13.28	1 563.56	376.87
7	14	1 070.91	45.11	185.55	76.49
8	18	4 063.80	14.50	873.32	225.77
9	13	1 818.76	10.60	452.26	139.90
10	6	889.36	19.00	317.20	148.23
11	12	2 350.00	32.19	497.58	195.83
12	8	1 665.53	54.34	701.22	208.19
13	23	6 613.98	15.95	1 160.06	287.56
14	12	2 644.65	21.94	1 106.14	220.39
15	19	4 416.32	21.63	1 758.26	232.44
16	9	1 762.76	33.94	633.51	195.86
17	5	1 319.47	117.65	509.60	263.89
18	6	719.50	56.86	225.78	119.92

[1]	KANG Jiawei, HUANG Xuankai, WANG Zhipeng, ZHANG Aizhen, MENG Fangrong, GAI Peng, BAO Junfu, SUN Kexin, SONG Shaokang, SUN Pan, CHEN Yichuan, ZHANG Lei, GAO Shengyue, CHANG Minghang. Estimation of Genetic Parameters for Growth, Reproduction, and Body Measurements Traits in Large White Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1936-1944.
[2]	PENG Peiya, CHEN Yuhan, YANG Long, WANG Ming, ZHAO Ruiting, HE Jun, YIN Yulong, LIU Mei. Research Progress of Copy Number Variation in Livestock [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1356-1369.
[3]	LEI Yanru, HU Xiaoyu, XU Chunhong, ZHANG Chenxi, DU Wenping, WANG Yangguang, LI Donghua, SUN Guirong, LI Wenting, KANG Xiangtao. Comparative Analysis of Growth, Carcass and Meat Quality Traits of Five Hybrid Combinations of Houdan Chicken [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1521-1535.
[4]	XU Donghui, XU Yuhui, LI Ruizhe, CHENG Haijian, MA Zhijie. Research Progress of Genome Copy Number Variations in Yak [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 933-943.
[5]	LIN Yan, HUANG Min, LI Xiujin, ZHANG Xumeng, HUANG Yunmao, TIAN Yunbo, WU Zhongping. Uncovering Genome-wide Copy Number Variations in 8 Duck Breeds Using Whole Genome Resequencing Data [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3700-3709.
[6]	ZHANG Xiaoke, LIAO Weili, CHEN Xinyou, LI Tingting, YUAN Xiaolong, LI Jiaqi, HUANG Xiang, ZHANG Hao. Genome-wide Association Study for Identifying Candidate Genes of Growth Traits in Duroc Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1868-1876.
[7]	BI Yazhen, SHANG Mingyu, HU Wenping, ZHANG Li. Correlation and Regression Analysis among Growth Traits and Association Analysis of TRHDE Gene Polymorphism with Growth Traits in Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1415-1428.
[8]	YANG Xinting, ZHENG Maiqing, TAN Xiaodong, ZHAO Guiping, HUANG Chao, LI Sen, LI Wei, WEN Jie, LIU Ranran. Genetic Parameters Estimation and Key Genes Identification for Meat Quality Traits of Fast-growing Yellow-feather Meat-type Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(9): 2416-2428.
[9]	HE Jieyu, WANG Binhu, LIAO Zhu, XIE Hongtao, YI Guoqiang, LIU Yuwen, AO Hong, TANG Zhonglin. Estimation of Genetic Parameters of Main Growth Traits in Landrace and Large White Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(8): 2115-2123.
[10]	QIU Hengqing, XIAO Shijun, GUO Yuanmei. Detection of Genome-wide Copy Number Variation Using Porcine 1.4M High-density SNP Chips in Bama Xiang Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(9): 2079-2088.
[11]	OUYANG Fengzheng, WANG Ligang, YUE Jingwei, YAN Hua, ZHANG Longchao, HOU Xinhua, LIU Xin, WANG Lixian. Genome-wide Association Study of Copy Number Variations and Quantitative Trait Loci Mapping to Identify Candidate Genes for Body Height Trait in Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(7): 1515-1524.
[12]	ZHANG Yi, BAI Hao, BI Yulin, LU Ao, HUANG Yanli, CHEN Guohong, CHANG Guobin. Research Progress of Copy Number Variation in Poultry Breeding [J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(11): 2633-2640.
[13]	HOU Haobin, LI Haijing, YANG Li, ZHANG Xinhao, SHI Tianpei, WANG Xinyue, ZHAO Zhida, ZHANG Li. Association between NCAPG-DCAF16 Region Polymorphisms and Growth Traits in Dezhou Donkeys [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(2): 302-313.
[14]	WANG Ligang, ZHANG Yuebo, YAN Hua, ZHANG Longchao, HOU Xinhua, LIU Xin, WANG Lixian. Identification of Candidate Genes for Porcine Bone Rate Traits by Genome-wide Association of Copy Number Variation [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(11): 2208-2214.
[15]	PEI Sheng-wei, WANG Li, CAO Xue-tao, LI Wan-hong, LI Fa-di, YUE Xiang-peng. Research Progress on Genomic Copy Number Variations in Cattle [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(5): 871-878.

Genome-wide Association Study of Copy Number Variation in Growth-Related Traits of Yunong-Black Pigs

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 6

References 47

Related Articles 15

Recommended Articles

Metrics

Comments

性状Trait	染色体SSC	物理位置/bp Position	候选基因Candidate gene
CC	1	157 232 630~157 498 487	/
CC	11	35 411 663~35 472 493	/
CBC	1	157 232 630~157 498 487	/
CBC	3	99 462 180~99 539 999	/
BF	15	110 808 122~110 878 014	/
BF	17	319 640~693 319	CLDN23